I run Izotope and Waves plugs, too. I think the issue is that - when you install the plugins - you are asked what version VST/AXX/Etc you want to install and VST2 is listed. However, even though you select the ONLY VST3 version, Izotope installs the VST2 version as well.
So I think what is happening is that the VST2 is blacklisted and NOT USED, but instead, Cubase has found your VST3 versions and is using them.
If you check the Plugin Manager you should be able to confirm this. Load an instance in a project that is working, and then open your Plugin Manager and find what version is being used. I think you will see it is a VST3 version.
Note, if you want to clear some room on your C Drive and make Cubase load plugins faster, find the folder with the VST2 versions and delete them. I’ve done this and found it was a help with Cubase.